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BaseRecalibrator warning - IndexDictionaryUtils

srdjansrdjan belgiumMember


I am working on a somatic pipeline (GATK 3.8, precisely 3.8-0-ge9d806836 ) and when running the following command:

java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R /ref/hg19.fa -I /mnt/6_realigned.bam -knownSites /genomes/dbsnp_138.hg19.vcf.gz -o /mnt/6_realigned.table -nct 8

I get this error:

Done. There were 1 WARN messages, the first 1 are repeated below.
WARN 15:27:06,646 IndexDictionaryUtils - Track knownSites doesn't have a sequence dictionary built in, skipping dictionary validation.

I looked around the forum and it said the file should be properly BGzipped and tabix indexed.

To make sure I unzipped the file, ran bgzip and tabix without any issues, getting dbsnp_138.hg19.vcf.gz.tbi .
Both dbsnp and its tbi are in the same folder.

Should I ignore this warning? What can I do to avoid it?


Best Answer


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